Evidence map›Paper›PMID 37645841›Full record

ArticlebioRxiv : the preprint server for biology2024

DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.

Simone Tiberi, Joël Meili, Peiying Cai, Charlotte Soneson, Dongze He, Hirak Sarkar, Alejandra Avalos-Pacheco, Rob Patro, Mark D Robinson

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Simone TiberiDepartment of Statistical Sciences, University of Bologna, Bologna, Italy.ORCID 0000-0002-3054-9964
Joël MeiliDepartment of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.
Peiying CaiDepartment of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.
Charlotte SonesonComputational Biology Platform, Friedrich Miescher Institute for Biomedical Research and SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
Dongze HeDepartment of Cell Biology and Molecular Genetics, University of Maryland, MD, USA.ORCID 0000-0001-8259-7434
Hirak SarkarDepartment of Computer Science, Princeton University, NJ, USA.
Alejandra Avalos-PachecoResearch Unit of Applied Statistics, TU Wien, Vienna, Austria.
Rob PatroDepartment of Computer Science, University of Maryland, MD, USA.ORCID 0000-0001-8463-1675
Mark D RobinsonDepartment of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.ORCID 0000-0002-3048-5518

Funding

A Modular Framework for Accurate, Interpretable, and Reproducible Analysis of Long Read RNA-Seq DataR01HG009937 · NHGRI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Michael Isaiah Love, Robert Patro · 2018 to 2026
$2.8M
NHGRI NIH HHS R01 HG009937
6 · The paper itself

Abstract

Motivation: Although transcriptomics data is typically used to analyse mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to study gene regulation and changes in gene expression production. Nonetheless, most methods for spliced/unspliced inference (such as RNA velocity tools) focus on individual samples, and rarely allow comparisons between groups of samples (e.g., healthy Results: Here, we present Availability and implementation:

Indexed as

Bayesian hierarchical modelBayesian inferenceBioinformaticsLatent variablesRNA-sequencing dataStatistical software toolTranscriptomics

Identifiers

PMID37645841
PMCPMC10462127

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.